Tool an In Flames are tied, in my opinion.
I've given Tool many, MANY listens, both sober and no, and I keep waiting for it to "click", but it never does. To me, they're just boring. But, I don't consider them over-rated for that. I consider them over-rated due to the fact that their fanbase doubled after hearing "Sober". It was those people that went and bought all the Tool t-shirts, and it's those people that consider Tool to be the greatest band ever. I've run into so many of those fucks, that I can't help but be influenced. To be that adored due to one song, or a series of videos, is to be over-rated.
In Flames is a simpler bit. They've not made a solid-all-the-way-through album since Subterranean. Many people mistakingly consider them to be the band that defined that Gothenburg sound, when we all know they didn't. By seeing a band like In Flames get big, it inspired other, mediocre bands to come out from the woodwork and try to something they're not. We wouldn't have half as much garbage floating around if bands like these weren't extolled to the nth degree.
And Cobain only killed that poppy, glam-metal bullshit of the 80s. I think we all appreciated that one.